Dear Jason,
Thank you. I am trying.
Sanjib.
On Wed, Aug 29, 2012 at 8:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Aug 29, 2012 at 11:03 AM, David A Case <case.biomaps.rutgers.edu
> >wrote:
>
> > On Wed, Aug 29, 2012, Sanjib Paul wrote:
> >
> > > So, at first I minimized my protein in sander.
> > > Then for nmdoe analysis I gave command like following:
> > > $AMBERHOME/exe/nmode -O -i nmdin -o nmdout -p protein.prmtop -c
> > > protein_min.rst -v vecs.
> > > My nmdin file is like following:
> > > normal mode analysis
> > > &cntrl
> > > ntrun = 1,
> > > maxcyc = 0,
> > > nvect = 12309,
> > > ismem = 0,
> > > ilevel = 6,
> > > ivform = 1,
> > > ntx = 1,
> > > ntxo = 0
> > > t = 300.00
> > > /
> > > But nmode is not running and showing a error like -
> > >
> > > Root-mean-square gradient of input coords is 2.05278199572829
> > > This is greater than the requested maximum: 1.000000000000000E-005
> > >
> > > Do I have to increase drms value? Actually I don't want to minimize
> > > the system. It is already minimized.
> >
> > No, it is not already minimized, at least as far as nmode is concerned.
> > You should carefully compare the energies printed out at the end of the
> > sander
> > run with those printed by nmode. There is probably some difference
> (which
> > could be caused by having different defaults in the two programs.) You
> > have
> > to make sure that the energy function is the same in the two programs
> (or,
> > use
> > nmode for both minimization and normal mode calculation.)
> >
>
> To add on a little here, scee and scnb, in particular, are different
> between the two programs, last I checked. I would also echo Dave's
> sentiments about using the nmode() function in NAB to do normal mode
> analysis.
>
> There is an example of how to use it that Dwight McGee wrote at
> $AMBERHOME/AmberTools/src/mmpbsa_py/mmpbsa_entropy.nab that shows a sample
> program using that call (and it also performs a minimization beforehand).
>
> You can also use MMPBSA.py directly to do nmode calculations on an entire
> trajectory (you can submit a single PDB file or restart file to MMPBSA.py
> with the -y flag to calculate only a single trajectory). If you specify
> only a complex topology file, then it will perform calculations on a single
> system (i.e., it doesn't *only* do binding free energy calculations).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Wed Aug 29 2012 - 09:00:03 PDT
